Searching Post-translational Modifications in Cross-linking Mass Spectrometry Data

2024 · doi:10.1101/2024.03.20.585841
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SeaPIC is the first XL-MS tool designed to identify post-translational modifications within cross-linked peptides, enabling new investigations into protein-protein interactions and structures.

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⚙ AI-generated deep summary by claude@2026-07, 2026-07-16 · read from full text ⓘ

The paper studies how to detect post-translational modifications (PTMs) in cross-linking mass spectrometry (XL-MS) data, which is used to investigate protein-protein interactions and protein structure. It introduces SeaPIC, a computational XL-MS tool designed to enable identification of PTMs in cross-linked peptides by addressing a major remaining challenge in the field. The key finding is that SeaPIC can successfully identify PTMs within cross-linked peptides that had not been previously discovered. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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Abstract

Cross-linking mass spectrometry (XL-MS) is a technique for investigating protein-protein interactions (PPIs) and protein structures. In the realm of biology, post-translational modifications (PTMs) play a critical role in regulating PPIs and reshaping protein structures. However, the identification of PTMs in XL-MS data poses a great computational challenge and thus remains unexplored. In this study, we introduce SeaPIC, the first XL-MS tool that enables biologists to investigate PTMs in PPIs and protein structures. Our experiments demonstrate the successful identification of PTMs within cross-linked peptides, which were previously undiscovered.
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Abstract Cross-linking mass spectrometry (XL-MS) is a technique for investigating protein-protein interactions (PPIs) and protein structures. In the realm of biology, post-translational modifications (PTMs) play a critical role in regulating PPIs and reshaping protein structures. However, the identification of PTMs in XL-MS data poses a great computational challenge and thus remains unexplored. In this study, we introduce SeaPIC, the first XL-MS tool that enables biologists to investigate PTMs in PPIs and protein structures. Our experiments demonstrate the successful identification of PTMs within cross-linked peptides, which were previously undiscovered. Competing Interest Statement The authors have declared no competing interest. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.

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